Chado Custom Tables

Functions
	chado_edit_custom_table (int $table_id, string $table_name, array $schema, bool $skip_if_exists=True)
	chado_create_custom_table (string $table, array $schema, bool $skip_if_exists=TRUE, int $mview_id=NULL, bool $redirect=TRUE)
	chado_validate_custom_table_schema ($schema_array)
	chado_get_custom_table_id (string $table_name)
	chado_get_custom_table_names ($include_mview=TRUE)
	chado_delete_custom_table (int $table_id)

Detailed Description

Provides an application programming interface (API) for managing Chado tables.

Function Documentation

chado_create_custom_table()

chado_create_custom_table	(	string	$table,
		array	$schema,
		bool	$skip_if_exists = TRUE,
		int	$mview_id = NULL,
		bool	$redirect = TRUE
	)

Add a new table to the Chado schema.

Deprecated:

Please use the new "tripal_chado.custom_table" service instead.

WARNING This function only supports creation of custom tables in the default Chado schema. Also, for Tripal v4 the $redirect and $mview_id arguments no longer have meaning.

This function is simply a wrapper for built-in database functionality provided by Drupal, but ensures the table is created inside the Chado schema rather than the Drupal schema.

If the table already exists then it will be dropped and recreated using the schema provided. However, it will only drop a table if it exsits in the tripal_custom_tables table. This way the function cannot be used to accidentally alter existing non custom tables. If $skip_if_exists is set then the table is simply added to the tripal_custom_tables and no table is created in Chado.

Parameters

string	$table	The name of the custom table.
array	$schema	An array contiaining a Drupal table schema definition
bool	$skip_if_exists	True to skip changing the table if it exists. False, to change the table. This may result in lost data.
int	$mview_id	If this custom table is a materialized view, the mview ID.
bool	$redirect	If this form should redirect to a new page.
Drupal\tripal_chado\Database\ChadoConnection	$chado	A ChadoConnection instance. If none is proivded then the default chado installation is used.

Returns

bool True if the table was created successfully, False otherwise.

chado_delete_custom_table()

chado_delete_custom_table

(

int

$table_id

)

Deletes the specified table

Deprecated:

Please use the new "tripal_chado.custom_table" service instead.

WARNING: This function only supports deleting custom tables in the default Chado schema.

Parameters

int

$table_id

The numeric custom table ID.

Returns

bool True if the table was sucessfully deleted, False otherwise.

chado_edit_custom_table()

chado_edit_custom_table	(	int	$table_id,
		string	$table_name,
		array	$schema,
		bool	$skip_if_exists = True
	)

Edits a known custom table in the chado database.

Deprecated:

Please use the new "tripal_chado.custom_table" service instead.

WARNING This function only supports editing of custom tables in the default Chado schema.

"Known" custom tables are tables that exist in the tripal_custom_tables already. If it is not in tripal_custom_tables, or the specified table does not exist, it will not attempt to make changes. It will also fail if the specified table is a materialized view.

Parameters

int	$table_id	The numeric custom table ID.
string	$table_name	The table name,
array	$schema	An array containing the Drupal table schema.
bool	$skip_if_exists	True if the table should not be changed if it already exists. False, to change it regardles.

Returns

bool True if the table was edited succesfully, False otherwise.

chado_get_custom_table_id()

chado_get_custom_table_id

(

string

$table_name

)

Retrieve the custom table ID of the specified name

Deprecated:

Please use the \Drupal\tripal_chado\ServicesChadoCustomTable::findByName() funct instead.

Parameters

string

$table_name

The name of the custom table.

Returns

int The unique identifier for the given table if it exists.

chado_get_custom_table_names()

chado_get_custom_table_names

(

$include_mview = TRUE

)

Retrieve a list of all Chado custom table names.

Deprecated:

Please use the \Drupal\tripal_chado\Services\ChadoCustomTable::getTables() function instead.

WARNING: This function only supports geting custom tables in the default Chado schema.

Parameters

boolean

$include_mview

True if the list of custom tables should include materialized views.

Returns

array An associative array where the key and value pairs are the table name.

chado_validate_custom_table_schema()

chado_validate_custom_table_schema

(

$schema_array

)

Validate a Drupal Schema API array prior to creating a custom table.

Deprecated:

Please use the \Drupal\tripal_chado\ChadoCustomTables\ChadoCustomTable::validateTableSchema() function instead.

This function can be used in a form validate function or whenever a schema is provided by a user and needs validation.

Parameters

array

$schema_array

An Drupal Schema API compatible array

Returns

string An empty string for success or a message string for failure